The Cycle
by Church Caboose
Summary: A squad fights for humanities survival on Earth against the Reapers and Covenant while Shepard discovers the legacy left behind by the Forerunners and attempts to stop the destruction of all Sentient life in the galaxy. DISCLAIMER: I don't own anything. Beta'd by Soul09981
1. Chapter 1 Only the Dead

**EDIT: IMPORTANT!  
**I will be rewriting Chapter 1 and will have it vastly different. I was planing on making edits here and there but feel it would just be better to scrap the whole thing and start again. THE REST OF THE STORY WILL REMAIN UNCHANGED! Aside from slight tweaks here and there _The Cycle_ will not change as a whole. Even this chapter will remain the same in regards to the time and place it occurs. This edit is because this is by far the worst chapter in the entire story. I did not plan it out well and it sort of turned into well bleh, I know for a fact though that the rest of the story is still a decent read and far better than many of the over done crossovers of this genre. So if you could please direct your attention to chapter 2 and come back to this later.  
For those of you who this may seem odd or annoying to I'd like to make it up to you, I present the greatest piece of crossover art ever produced in return for your forgiveness :) art/First-Contact-The-Covenant-161512711 this is what I would have wanted the cover to be.

Ch 1

Only the dead

Alliance Space

Earth: Reaper Invasion

Hell was a simple word to use; Church had often used it to describe many things, boot camp, his parents, the mess hall. Only now did he fell the true meaning of hell. He rubbed the grime from his eyes still red and sore from exposure to foreign debris. He looked around attempting to regain his bearings. 'Ok.' He thought, 'time to find out what the hell hit me.'

He looked around from where he had landed. What used to be a small community on the English country side was now devastated. It appeared as if a war had happened. All around it smelt of death and destruction. The fields were aflame with bodies and other vehicles on the road burnt to a crisp. He began to remember what happened, 'we were on our way back to base from the bar…' he stopped and turned. 'Oh god please let them be all right'.

"Erin! Manny! Are you alive?" he quickly turned around and looked back at the crashed taxi which would never be able to fly again. Somehow he had been thrown nearly 20 feet from where it landed. "Damn it if you guys are dead… shit!"

Church ran towards the car and searched the wreckage finding what appeared to be a large mass that resembled his squad mate Erin. He quickly turned over the body, it was Erin. "Shit shit shit shit," He felt for a pulse and breathed a sigh of relief when she began to come back to conscious.  
"You gave me a heart attack for Christ sake!"

"Well it was your terrible driving that caused it, where are we any way?"

"A few miles outside London, I think we might have hit a bird."

"Why is it always me who you forget about never Erin but me," Came a voice on the other side of the car. "Tell me what did I ever do to deserve this?"

"Christ I forgot about Manny."

"Oh no its fine Church, just leave me to die here in the mud that will be fun," came a sarcastic and agitated Manny.

_VVVVVVVVVVRRRRRRRRRRRRRRMMMMMMMMMMMMMM_

"That's one fucked up bird." Manny exclaimed viewing what had made the monstrous sound.

At once everyone looked up and viewed what had caused the destruction all around them. It was incredibly large, as tall as a skyscraper, and was just plan massive. It resembled what could only be described as an extremely large cuddle fish.

"Is that…"

"Yeah I think it is… a Reaper."

They had all learned the stories of the brave Commander Shepard. He was the first human Spectre, and the savior of the citadel council. There wasn't a child alive human or otherwise that didn't know the name Shepard. His story as an Alliance war hero had convinced Church to first join the Alliance.

When Shepard had become the first human Spectre, Church jumped at the chance to follow in his footsteps signing up for the N7 program. Against all odds he had been able to not only meet but excel all of his instructors' expectations. Church had graduated top of his class and been placed in a squad that consisted of himself as squad leader, Manny as his Staff Lieutenant, and Erin or the rookie as a 2nd Lieutenant along with a few others. None of Church's training could possibly prepare him for what now stood in front of him, if you could say it was actually standing.

"I don't believe it, the crazy bugger was right!" Shouted Manny who was still wincing from the pain of the recent crash, the Reaper was several clicks and with it's back facing them.

"Must have flown down and shot the road up all to hell." Manny continued

"Its heading for London, Church you'd better radio in tell command what happened." Erin said joining Church on the other side of the car by Manny.

"Yeah on it," He immediately pulled up his omni-tool and went to the military only channel.

"I think they already know," Manny had finally stood up and began pointing towards the sky above London. Dozens of the Reapers were descending from the sky in an almost uniform fashion. All of them were attacking indiscriminately firing their Mass Effect weapons anywhere over the city.

"This can NOT be happening!"

"Alright let's check around for survivors and then get back to base ASAP," Church exclaimed quickly taking control of the situation. He checked the cab once more to grab supplies. Luckily they had brought their rifles to go shooting behind their favourite bar. Church wished more than anything to be back at that bar not seeing the destruction occurring around him.

"Church you may want to see this." Erin said pointing to the sky and then her omni-tool. "We've got slip space ruptures, the Covenant is here too."

Church looked up to the already cluttered sky to see large dark blue portals open up just past the atmosphere. Out of the slip space ruptures came large Covenant Battle Cruisers entering orbit. If this wasn't bad enough an even larger Super Carrier quickly joined them appearing to be the flag ship of the covenant fleet

"Right so anyone up for just high tailing it to Cuba for the end of the world?" Manny said seemingly serious.

"Not funny" Said an aggravated Erin looking cross towards her squad mate.

"What the Alliance barely survived the Covenant war how can we hope to take them and the Reapers on? It's not like the Covenant will just out of nowhere start fighting themselves or the Alliance finds some sort of super weapon!"

"You're probably right Manny, but I don't plan to just watch Earth burn from Cuba. Now let's get going." Church said coming up and slamming an assault rifle into Manny's hands. "Now if there aren't any more bright ideas I'd like you to cover our six."

"Aye sir" Manny and Erin said in unison. They both checked over their weapons with Erin carrying an M-22 Eviscerator as a side arm and her highly expensive and customized Black Widow. Manny preferred a much lighter approach as he was the squad's only Vanguard biotic member, he carried an M-15 Vindicator upgraded to be lighter and fire faster. He also carried a Covenant plasma pistol.

"Good, I'll take point we'll keep moving towards the city and check for survivors. Erin you keep your eyes up ahead and give us a heads up if we get incoming, Manny check everyone we pass. Make sure they're not breathing."

"Aye sir" they said in unison again.

"Good now let's move it!"

And so they went, checking every downed car and every single body down the road that led to the city. And wasn't until they were nearly in the city that they encountered any sort of movement.

"Church I got, some sort of Reaper ground soldier coming our way!" Erin said looking down the scope of her Widow. "They look almost human!"

"What do you mean almost?" Manny said sliding behind a fallen red sports car in preparation for a gunfight. "And what kind of fire power are they carrying?"

"None, they're just running down the road searching for survivors. Wait they stopped, oh my god, Church they're attacking civvies."

"Can you get a shot?"

"No, god damn it they went behind a damn sky car!"

"Let's go then, Manny you're with me, Erin try to take them out from here if you can!"

They quickly sprinted towards where the husks had disappeared. As soon as the husk heard them coming they quickly looked over and seeing two new live humans quickly charged. Manny and Church slid into cover behind a fallen tree and began to open fire. From behind Erin was able to drop two before they got close to them. The entire group was gone in no more than a minute. Manny quickly checked behind the car the husks had been hiding and saw what had gotten their attention.

"Church you may want to see this."

Church came over and inspected the scene. The husks had attacked a women no older than 20. She lay there on the ground clearly beaten to death. But the girl is not what made the scene shocking there next to the girl was laying a dead Elite. A dead Elite was not shocking in on itself, any Alliance Marine squad could have taken at least one down. It was the fact he had burn marks all over his body. The burns were not from Alliance or Reaper weapons but from Covenant plasma rifles.

"What do you make of this?" Manny questioned squatting to inspect the carcass more closely. "Could have been some heavily equipped squad, one of ours maybe."

"No, it doesn't add up. All Alliance personal had standing orders to return any Covenant weaponry. There were too few that kept any plasma weapons. And besides they were only able to keep small side arms, like your pistol."

"Well then what do you suppose he went rogue and tried to kill his buddies?"

"Hell any war could make you go crazy, our friend here could have just finally cracked."

"I'm not buying it."

"Not our problem right now anyway let's move."

"Hey what did I miss?" Erin said catching her breath from her slight jog over to their position.

"Just a dead Elite you know the usual."

"One of ours did it?"

"Nope plasma weapons did him in." Manny said standing up and reloading his rifle.

"Alright enough rest let's move, we're almost in the city and we still have a war to fight." Church said pointing to the city. "And I don't intend to win it out here."

**AN: **I'm going to be placing all my future notes at the end and I'll be making them smaller. To those of you who are new to _The Cycle _the story starts to pick up in the next chapters this was a way to help introduce where this will be heading so please read on before you criticize. Please review if you like and let me know what you think I should change.


	2. Chapter 2 War and all its pleasures

Ch 2

War and all its pleasures

Earth System Alliance Space

Harvest: Covenant War (4 months before Reaper Earth Invasion)

"Am I the only one who liked it better when the enemy wasn't beating us?" Shepard said as the Normandy came out of the Mass Relay in the system of Harvest.

"I don't know Shepard," Said a sly Joker attempting to lighten the depressing mood in the Normandy's cockpit "They could prove to be a new challenge for you."

"Not funny."

"Hey couldn't hurt to try. Do you even know what we're up against here? Intel said and I quote 'Giant squid faced monsters on shark ships'."

"Actually Jeff the Intel report was not so humorous." EDI's hologram said appearing on the cockpits terminal

"Yeah I know I was just trying…"

"To lighten the mood we got it," Shepard finished for him "Now please can I get some quiet for a moment!"

Shepard leaned back into the copilot seat and closed his eyes for a moment. It was less than 2 months ago when he had destroyed the collector base and cut ties with Cerberus, Most of the crew he saved from the collectors and his squad went their separate ways. That left Shepard with an illegal AI and a highly advanced warship with only him and Joker to run it. So with no other real options he gave it back to alliance command. They in turn forced him to take mandatory "shore leave" while they assessed his ties to Cerberus.

Meanwhile the Normandy had been broken down and rebuilt by Alliance command, with a few new upgrades. Somehow EDI had been able to pose as a simple VI in order to not be decommissioned. Alliance command had decided to leave Jeff "Joker" Monroe as the pilot of the Normandy as he was the only one who flew both the SSV and SR2.

So when a border colony near the edge of the galaxy came under attack by an unknown alien force, the Alliance command was dumbfounded. Another first contact war and this time they were facing a highly advanced foe. So Shepard had been reinstated mainly due to the lack of resources and Admiral Anderson's pull. And so Shepard had been assigned to reconnaissance to see what this new Covenant could do.

"Shepard you have a transmission in the war room."

"Right, thanks EDI."

Shepard walked down the CIC past the crew who were hurrying about their duties. He made a notice towards Specialist Traynor who had been assigned as his Comm. Specialist. After passing through the conference room he reached the War Room. The entire ship had been intended for Anderson to use as his personal HQ, of course at the time he expected to fight Reapers. When this new threat arrived Anderson went to the citadel to gain support against this unknown enemy in case it escalated to a prolonged engagement.

Finally Shepard reached the war room's holographic communication terminal. A blue shaded holographic Anderson was waiting for him.

"Shepard, I hope I'm not interrupting."

"We're still in route, anything to report Anderson?"

"Well Udina and I have met with the Council; they want a better report on the situation. Frankly I don't blame them, we were completely blindsided by this 'Covenant'. Hell we don't even know how their tech works."

Anderson was referring to the oddity of the alien ships and weaponry. When the colony ship in orbit over Harvest had spotted the lone scout ship the crew was flabbergasted. The alien vessel had not entered through the Mass Relay nor had they entered through any known means of FTL. There were no readings of any element zero on the entire ship. Nearly every technological advance in the past century was only possible due to element zero physics. And yet an alien race or races had been able to evolve and have absolutely no trace of the stuff.

"I'm a bit confused myself Anderson, why exactly are they attacking a colony at the edge of the galaxy? It barely had a few thousand colonists."

"We don't know. We had attempted a peaceful first contact scenario, standing orders were to assume aggression, but no shots were fired from our side. It appeared to be going well, the ground team at the rendezvous said first contact started off without a problem. The aliens or what they described as 'big smelly apes' had cooperated. It wasn't until they began making demands for the entire planet that all hell broke loose."

"They asked for the entire planet!? What would make them so bold?"

"More advanced weaponry, greed, hell they may have just been bored."

"You don't think it could be another ploy by the Reapers?"

This idea had never crossed the Admiral's mind; he believed Shepard about the Reapers and attempted to prepare the galaxy that continued to deny the Reapers existence. After Shepard had destroyed the Collector base Anderson assumed the Reapers would stop toying and begin their full out invasion, it was conceivable that this was just another Reaper plot. After all they didn't seem to be stopped by anything.

"No doesn't add up, nothing we've seen from the other cycles suggest anything of this technological tier. We're dealing with some other faction."

"Shepard ETA is 5 minutes." Joker said over the intercom.

"Good luck Shepard and remember we're counting on you to end this, and hopefully soon before the Reapers arrive," Anderson said giving a stiff salute.

"We'll have won before you know it," Shepard replied returning the salute.

Anderson vanished from the holographic terminal and Shepard turned to return to the CIC. As he walked he asked loudly to be heard by EDI if Lt. Commander Ashley Williams and Lt. James Vega were ready.

"Affirmative Shepard they are heading down to deck 5."

Shepard had been allowed to pick and assign his own crew for the duration of this conflict. This was mainly due to his outstanding service as a war hero and his ability to get results when left to his own devices. He felt that this also allowed the Alliance Brass to skip over the AI and go along with the VI story, despite EDI's best attempts it was still very much obvious that she was no standard VI.

"Good I want them ready to go ASAP." Shepard stepped into the elevator which EDI automatically brought to deck 5. Upon reaching the armory Shepard began gearing up while the new pilot, Cortez, explained the Normandy's new shuttle bay.

"And that's pretty much it, still very much the same Normandy, just flying Alliance colors."

"Thanks Cortez, you ready to roll?"

"Aye sir, about to begin pre-flight checks,"

"Well Shepard didn't expect you to drop the Cerberus colors so quick." Ashley Williams said stepping over from the far side of the bay.

"Ash, good to see you too,"

"The Lieutenant here was just explaining to me how the Alliance just allowed you to take their most valued bird."She said in a slightly disgusted way

"Sorry sir she insisted," James said defensively coming up behind her.

"Can it, Ash quit bitching about Cerberus, both of you go wait in the shuttle," Shepard ordered snapping at both of them as instinct quickly took hold and they followed the orders of their commanding officer.

'I honestly don't know why I bothered to bring them along' Shepard thought quietly to himself as he walked to the Kodiak shuttle. He knew exactly why he had brought Ashley and James along. Shepard had few allies left in the Alliance, with many wishing he had remained dead. James was the only enlisted he knew that didn't treat him as an outsider. And Ash had always been a pain but she was still a hell of a soldier and an old friend.

"Cortez lets hit it."

"Aye sir,"

The shuttle left the Normand's bay doors as the ship exited the Mass Relay into the mass confusion that was the colony of Harvest.

'Another day another war' Shepard muttered to himself.

**Author's Notes:**Woohoo finally finished with Ch2 and the story is in full swing. I wanted to make Ch1 to be a slight prelude, mainly cause I wanted to write the most exciting part of the story first. But up next there will be action and adventure. I want to say that this Shepard is Paragonish as in he won't be needlessly kill anyone. However he's what I feel Shepard would be at this point, he feels unappreciated, slightly betrayed, and tired from having to save the human race so many times (gahh Chief never bitched about it haha). And the first contact scene is based off the book _Halo: Harvest_ but I will change it up as I see fit. I also had him snap at Ashley because everyone feels she became a bitch in ME3 anyways. So if you have any thoughts comments concerns PLEASE pm me or review I'm all ears and again no unneeded rude comments.


	3. Chapter 3 Truth

Ch 3

Truth

High Charity

23rd Age of Doubt several light years outside Human controlled space

After eons of sleep the AI Mendicant Bias awoke from his extended slumber. Before him in the control center of the Forerunner Dreadnaught he saw the three misguided San 'Shyuum. They came to him believing that the Philologist would "interpret" what he, their Oracle, believed the Covenant's actions should be. The grim reality was he cared not of what happened to the Covenant, only that their mistake be corrected.

"For eons I have watched. Listen to you misinterpret. This is not Reclamation, this is Reclaimer!"

He watched as the fools panicked unaware of their mistake. The aliens thought the newly discovered Humans were relics of Forerunner creation. Their luminary had given them the symbol for Reclaimer and they saw only relics. Mendicant did whatever the AI equivalent of a chuckle was and began to activate the dreadnaught's engines. He cared not for the fate of High Charity which the dreadnaught powered.

"Is he… no that would destroy High Charity," The Vice Minister of Tranquility stammered. "Minister we must do something!"

Mendicant did not give the San 'Shyuum another thought. He would fix their mistake and provide Humanity with the path the Forerunners had chosen for them. However deep inside the walls of the vessel worm like creatures called Lekgolo, which tunneled through the ship in hopes of learning more from it, began to die as the energy and heat ran from the engines throughout the rest of the ship. Seeing their fellows die the Lekgolo attempted to stop the ship before it would destroy them all.

Meanwhile the three San 'Shyuum sat there dumbfounded not knowing what to do. The Philologist began spewing out prayers and urged the Oracle to continue with its task. It wasn't until the Lekgolo short-circuited the AI that the Philologist was able to overcome his awe and disconnect Mendicant from the dreadnaughts controls, saving all of High Charity in the process.

"This…, this changes everything. Every text and knowledge gained from the Gods about their Journey could be false," the Philologist stammered.

"Yes, this could completely destroy everything the Covenant stands for and completely ruin the balance of power," Fortitude explained. "So we must never let the knowledge here become known." He said aside to his companion and co-conspirator the Vice Minister of Tranquility.

"Too much planning and work has gone into this plan, we cannot allow the Covenant to splinter now."

"I agree with you completely, however what shall we do with the Philologist?" Tranquil asked puzzled as to how to best silence him.

"Well we need a party of three, why don't we offer him to be our third Hierarch." Fortitude said more as a command than a question.

"If you find it to be wise."

"Calm yourself now Philologist, the danger has passed."

"I know that but what should we do of the knowledge gained here? The Gods left these Reclaimers as their successors."

"We shall keep it secret, if this knowledge were to become known the power of the Prophets would be no more. So the Vice Minister and I are willing to offer you a deal. Say the Oracle chose us to replace the Hierarchs and we shall allow you the third position."

"But what of these Reclaimers?" Tranquil interjected.

"Every last one of these Humans shall die; we shall say they were responsible for the destruction of relics that will justify their extinction."

"Fine then let it be done, so long as the Covenant survives," the Philologist said.

"Excellent now let us hurry there are many preparations that must begin."

Alliance Space: Harvest

4 Months before Reaper invasion

"A simple recon that's all it was supposed to be. Land on Harvest check out the ground force while the Normandy surveys the damage how hard could it be?!" Vega cursed as he Shepard and Ashley ran from heavy enemy fire. They scurried through the streets of the small colony town trying to find somewhere to hide. Unfortunately everywhere they turned there was another baddie waiting for them.

Finally they were able to duck inside a small apartment. Being able to finally rest and catch their breath Shepard ordered Ashley to keep an eye out while he and Vega secured the house.

"So Shepard, you miss the Collectors yet?"

"About as much as I miss being dead. Left room is cleared."

"Huh at least we could kill a couple of Collectors. I swear those damn, what did I call them, Elites never seem to go down."

"We did our recon let's just try to get to the LZ in peace. You check the closet?"

"No I thought you did."

James and Shepard both turned towards the closet at the back of the farthest room in the house. Shepard motioned for James to open the electronic door while Shepard pointed his Mattock toward the door. The door slid open showing only darkness, Shepard quickly switched on his light only to startle a small ugly ape-like alien. It jumped and squeaked placing its hands in front of its face with its only weapon, a needler, pointed in the air.

Shepard hesitated, the small Grunt looking almost innocent as if he didn't want to kill anyone. After a mere second Shepard breathed, aimed, and clenched the trigger scoring a headshot instantly killing the alien. As weak as the Grunt looked he could still kill and Shepard wouldn't dare take a chance of his squad getting hit by one of those.

"Shepard, everything alright?" Ash said hailing him over the omni-tools radio.

"Yeah just a small one that got left behind."

Shepard and James went to rejoin Ashley in the main room of the house.

"Any movement?"

"Got three scouts, the Jackals I think. But we lost the main force."

"Right, James contact the Normandy tell Cortez he'd better be at that LZ by the time we are."

"On it."

"Think you can take out those buzzards from here Ash?"

"Child's play."

Ashley rested her Viper on the windowsill, aiming for the skinny heads of each Jackal as they searched the wreckage on the street for any survivors. After quickly practicing moving from the first to the second and third she fired 3 consecutive shots with the first two hitting their marks. The third missed and hit the Jackal's shoulder. After noticing her error she quickly aimed and fired again this time taking out an eye.

Noticing that his comrades were being attacked a lone Jackal sniper began to scan the area from atop of the Human made tower. He quickly spotted where the shots that killed his kind originated from and pulled his beam rifle to bear. He quickly spotted the Human female and fired.

Ash ducked down as soon as she heard the beam hit. The sniper had missed her by mere inches and she didn't feel like giving it another shot.

"Sniper up top."

"Right, I'll run out give it something to shoot at. Ash, take him out before he takes me out. Once he's down it's a straight shot to the LZ." Shepard gave the squad his orders and moved into position by the door. After quickly opening it he sprinted out and ran for the nearest cover. As he dove behind a fallen wall he heard the familiar sound of his shields failing.

Ash watched as Shepard quickly ran out of the door before she began to aim for the sniper. After several moments she spotted him and zoomed in on his head. The Jackal had his eyes set on Shepard as he dove for the wall. Seeing his prey might get away he hastily fired before an accelerated bullet punched through his skull.

James ran out of the apartment sprinting for his fallen comrade.

"Commander you hurt?"

"Just nicked me, shields took the brunt of the force."

James reached Shepard as he began to sit up. The shields had indeed protected him from the blunt of the damage, however Shepard's leg had a small circular burn that went through most of the armor and had left him with a small burn on his leg.

"Should be fine so long as I don't get hit again. Where are we on the pick up?"

"Cortez found a field a few klicks away," James said assisting Shepard to his feet.

"Alright let's move it before their buddies come looking," The two began moving through the debris on the road as Ash jogged to catch up. The squad walked in almost complete silence focused entirely on getting to the LZ. They were able to go down several blocks without running into any hostiles. After avoiding the first patrol group they saw since the Jackals, James spoke up.

"You know I've been thinking this attack doesn't make any sense. Why go through all this trouble to have a ground invasion when you could wipe out all the forces on this planet easily from orbit."

"He's right it doesn't make sense," Ashley said pondering over James remark.

"The way I see it they're probably looking for something here."

"And what would they be looking for James?" Shepard questioned having his curiosity peeked.

"I don't know but I got a feeling command does."

"Just focus on getting to the LZ, then we'll worry about conspiracies."

High Charity

9th age of Reclamation several light years outside Human controlled space.

Fortitude gleamed as the millions of aliens watched as he and his fellows were declared High Prophets. Thousands had turned out for the ceremonies; there was even a Yanme'e queen in attendance. At last the Covenant would be under strong leadership. The lesser species would follow their will without question, and with the Great Journey soon at hand he would be a god.

The truth of the Humans could never be revealed. This was imperative above all else, as it would see the fall of the Covenant. This is why he adorned the name Truth, to remember the lies he must tell for the greater good.

'The only thing that may pose a threat are the Sangheili,' he thought to himself. 'Every other race is knows obedience, but they have always been in some form of power. They will question the reason of this war eventually. Hopefully by then it will be too late.'

The mass of life below the three prophets from their high throne room began to cheer as they came into view. Truth cleared his throat and knowing nearly everyone in the Covenant was watching, began to talk with a cold calculated demeanor.

"The time of Doubt is over, soon the Great Journey shall commence. All of those who follow the path shall reach salvation. Those who hinder it shall meet their doom by our hand! These Humans are nothing more than a pest, their existence shall plague this galaxy no more and the relics they do hold will return to the true inheritors of the Gods, the Prophets!"

Truth smiled at himself, he'd given the people what they wanted. An end to all the searching that began ages ago was now culminating. The Humans would burn and this Harvest would show them the key to unlocking how the Forerunners reached transcendences. The Great Journey was inevitable and nothing would prevent Truth from claiming the title of God.

**AN:**So this is starting to look good now, didn't like writing the first part but it was necessary to help explain some of the back story for those who don't know it. Well like always please review and help me out. Tell me what you think and how I can fix the writing. Its weird switching from Mass Effect to Halo as they are so vastly different. I feel I do better writing when I use just my head, but when I try to copy from another story or novel like I mainly tried to do in the first part if feels clunky. So if you have any tips please feel free to share.

Coming up next on the Cycle: The Covenant begins their search for the Rings, Shepard finds out the point of their invasion. And we get to see Church and his squad from Ch 1


	4. Chapter 4 Conspiracies

Ch 4

Conspiracies

Alliance Space: Harvest

4 Months before Reaper invasion

The squad had just watched the shuttle land when they came under heavy fire. The aliens used some sort of mortar like tank along with dozens of infantry. They barely managed to escape alive, the shuttle was skimmed by a shot from the Wraith tank as it took off.

Unfortunately their trouble wasn't over yet. Shepard began to worry as he sat down in the cockpit of the Kodiak shuttle. Cortez worked furiously at the controls attempting to lose two Banshees following them.

"They don't give up easy do they?" James said strapping in his seat at the back of the shuttle.

"I don't know if I can shake them Commander."

"Contact the Normandy; tell them we need some cover." Shepard said beginning to sound worried. He had seen one too many near death encounters for one day. Joker's voice began to sound throughout the shuttle

"Shepard I hope things look better on your end than ours."

"Not exactly, sending you our coordinates, we got lightly armored baddies on our tail."

"I'll see what we can do about that," Joker said as the communication cut out. The occupants of the shuttle all panicked as one of the Banshees scored a hit with its plasma cannon. Cortez was attempting to out maneuver the ships, but they seemed to be able to follow him move for move. Suddenly one of them engaged a boost and zipped in front of the Kodiak.

It continued until it turned towards the sky and came back down heading straight for the shuttle. The Banshee began to initiate the targeting on its fuel rod cannon, soon the Human ship would be another crater in the ground. The icon turned red and the Elite pilot smiled as he slowly savored the easy kill. But before he could pull the trigger his ship was blasted from the sky. His wingman quickly followed and the Normandy SR-2 emerged from the clouds Thanix Cannon showing from underneath.

"Damn good save Joker you had me worried for a sec." Shepard said smiling for the first time that day.

The Kodiak began its docking maneuver and landed safely inside the Normandy's bay. The exhausted squad stepped out and headed for the elevator for a much needed rest. Cortez began to assess the damage of his shuttle. It would take weeks to repair, and even then there would still be visible damage.

"I don't know who these guys are but they sure as hell know how to fly," Cortez muttered to himself.

"Don't worry about, slap on a new paint job and it'll be fine," James said slapping Cortez on the back laughing, before continuing for the elevator.

Shepard stepped off the elevator on the 2nd deck and headed directly for the war room. After reaching the communication terminal a holographic version of Admiral Anderson appeared.

"Anderson"

"Shepard I hope you have some good news."

"I'm having EDI send you all the data we've retrieved. So far the only concrete information we've gotten from their communications is their name, the Covenant."

EDI's voice carried out through the room being heard by both Anderson and Shepard. "We've also been able to uncover they are some sort of religious alliance of several different species. I've been able to obtain specifics on most of them."

"How many alien races are there?" Anderson asked baffled as to how they would survive.

"Six in total have been seen in combat but they may be led by some other race."

"I'll have EDI send you and the Council everything we have on the aliens and their ships. Any word on whether or not we have their fleets?"

"Yes they're actually helping us this time." Anderson said with a hint of annoyance in his voice. "We're expecting their ships to help defend key relays and provide some additional support. Not sure how much help that may be considering this Covenant may not even know how to use Relays."

"Well that's a first, why would they help us with this but not the Collectors?" Shepard inquired puzzled about the Council's motives.

"When our colonies were first disappearing it was a mystery as to who was responsible. At the time only rumors about the Collectors arose, we had no proof of any sort of disappearance other than the lack of people. This Covenant wasn't quiet, they didn't even attempt to hide. They came right at us, and they aren't taking prisoners like the Collectors. According to your reports and several others they've begun to destroy the planet entirely."

"That's something I wanted to ask you Anderson, according to the orbital drone scans they're focusing their military somewhere in the western hemisphere. That's the opposite side from any population centers or valued targets."

"Yes I may have a reason for that. Soon after we received word of the Covenant's arrival I was informed of some sort of highly classified project occurring on the planet's surface."

"What type of project?"

"I don't know there were only a handful of individuals who knew about it. All I know is that there is a base over some sort of ancient alien ruin." Anderson continued to explain while a holographic map of Harvest appeared next to him. It zoomed in on the continent in the western hemisphere. It continued into some flat hilly terrain. There in the middle of nowhere was a small Alliance military outpost.

"What could be there that the Alliance needed to hide?"

"I don't know Shepard but you've been ordered to go and find out. We had contact from a squad still in the facility; we need you to pull them out along with any research there. We need to know why the Covenant want this planet so bad and more importantly what they want in that facility."

"Understood Anderson," Shepard said stepping back and walking back towards the elevator. 'Glad I didn't bother to take off the armor.'

"EDI get the squad ready and in the bay, I want the Normandy to drop us off just outside the enemy's front line."

Harvest: Alliance Military Research Outpost

Church ducked back behind his wall as plasma raced past his head. There was only one way into this outpost and the Covies kept trying to pour in. He and part of his squad were, as far as they knew, the only ones left alive after the Covenant overran the outer perimeter. All that remained was himself, Erin, Manny, and Samuel with the rest of their squad lying dead outside.

At the moment every one of them focused their fire on the caved in metal door. Wave after wave of the Grunts came in never seeming to end. Church gave the order to fall back deeper into the base. The squad came to an elevator that would lead them underground.  
"Erin get the elevator open, Sam cover us." Church shouted as he and Manny physically shut the door to the elevator room. Sam continued firing through the crack as the other two struggled to firmly shut the door. He fired a biotic singularity out blocking the front hallway and preventing any more Grunts from entering. Church and Manny gasped as they finally shut the door. They leaned against it to catch their breath as all of them took a slight breather.

"The elevator Erin?" Church said coming over his squad mate kneeled on the floor trying to hack the door with her omni-tool.

"We never had clearance to go past the front door, I have to go through dozens of fire walls just to open the door, and then there's the control…"

"I don't think we have that kind of time," Sam said pointing to a screen in the corner of the room. It showed the room before them with dozens of the Grunts coming in followed by the much larger Elites. One Grunt pulled out some sort of device and began to cut the door with a flame of plasma.

"Got it," exclaimed Erin as the elevator doors slid open. They all piled in as Erin pressed one of only two holographic buttons used for control. Immediately the Elevator began to descend deep under the ground.

"This is bull-shit," Manny cursed under his breath "they make us defend some secret bunker at the ass end of the galaxy and they don't even tell us why."

"Manny!" Church glared wishing his subordinate would fall in line.

"No he's right Church," Sam said coming to his defense "for all we know these guys are trying to find lost property."

"Doesn't matter anyway, once they get down here we're all dead." Erin piped up causing the car to become gravely silent.

"Were we able to get a signal out?" Church asked to no one in general as he checked his omni-tool. After several minutes of fiddling with the radio the device began to talk.

_"This is Commander Shepard, can anyone respond?"_

"Commander, this is Lieutenant Commander Church Reynolds. Damn are we glad to hear from you."

_"We're on our way to your location, what's the situation?"_

"Situation? Sir we're fucked there are only four of us left and they've completely over run the base at the ground floor. We were forced to retreat underground."

_"I need you and your squad to make sure that elevator doesn't come back up until we reach it."_

"Understood sir, you're here for a rescue right?" Church said looking over his squad. They were in no shape to fight, in a single battle they lost nearly everyone they knew.

_"We're also here to gather intelligence, I need you to stay where you are. We'll come to you."_

"Aye sir," the radio went dead. The mood in the elevator soured even further. Manny looked pained as if he was abandoned and alone. The rest of them tried to hide their emotions but they all showed the same face. They were forced to keep fighting after they had already lost this base. And it didn't look like they would make it home any time soon.

**AN:** Right so I'm only going to put my notes after I have each chapter beta'd. Please review and comment if you like the story, or if you have any suggestions.

Now here is a fun part, in order to get more and more people to review and comment on the story we're going to have a contest. There will be several points in this story that will require a paragon or renegade choice to be made along with several other key choices. I would like you the reader to tell me what the choice should be. Based off the amount of responses I get for a choice it will be either one.

For the first choice, Mass Effect has several love interest as we all know each of us has our favorite. I feel that if the love interest is not to our liking or not done right then it can really hurt the story. This option wont affect it much but a small bit here and there can really help drive it along. So I would like to have the love interest be the most popular out of the people reading this (Even though there are only a hand full of you)

To those of you who have no idea of the love interest the choices are...

Liara- Hot blue Asari scientist

Ashley- Career soldier hates Cerberus

Tali- Quarian shy always in a suit

Miranda- Hot test tube baby

Jack- she's well Jack

Cortez- Gay pilot actually one of the best new characters in ME3

If there is anyone else you think ol Shep should romance let me know. It won't affect the story too much but can help or harm it based on the character. I'll keep who it is a mystery until the end where they will be romanced and have the whole scene and blah blah.  
If no one votes I'm going with my favorite Liara, so if you want someone else or hell you're just bored, review and tell me what you think about this.

This whole viewer choice thing is experimental, it will include choices that were found in ME3 along with a few thrown in to effect the Halo aspect. If i receive too many bad reviews for this idea it will be taken out and I will simply use my own choices made through out the story. I think this will be fun as the reader will be able to see where their idea was placed into the story and so on. Please review and ask any questions you want I will do my best to answer them.


	5. Chapter 5 Forerunner

Ch 5

Forerunner

Harvest: Alliance Military Base

Shepard jumped out of the Normandy's hanger bay, landing hard on the barren rock. Behind him came Ashley and James both grunting as they hit the ground. The Normandy closed it's bay and pulled up as it headed back into space.

"Alright we go in grab the data and rescue the survivors," Shepard said addressing his squad

"Yeah, piece of cake," James exclaimed as he scanned the area. The squad began to move west towards the Alliance base several klicks away. Shepard couldn't risk taking the Kodiak in closer as it was still damaged from their reconnaissance mission. The Normandy had to drop them far enough away so as not to be seen by the Covenant. As such they were forced to walk the distance hoping they would remain undetected until they reached the base.

"Any idea what kind of resistance we'll run into?" Ashley asked with a crackle of fear in her voice.

"Expect heavy resistance last scan showed several dozen aliens."

"Are we getting any sort of reinforcements?! These guys aren't outfitted like your average merc," James exclaimed

"Alliance is still trying to prepare the fleet, this was a small colony not enough to risk any more lives over," Ashley answered

They came to a stop at the top of a hill overlooking the facility. Shepard signaled for them go quiet. "Enemy up ahead, looks like they're digging in trying to stay awhile."

Ashley pulled up her sniper rifle looking down the scope she could see exactly where the Covies were. All of them were located in the front the Alliance base setting up defensive positions. There were four of the jaw split aliens, Elites as James called them. One, with white armor and helmet decorated with some red markings, was barking orders towards his lackies. The three lower ranking Elites, who wore less eccentric armor making them look more stream-lined similar to a shark, were carrying their fallen brethren to an awaiting drop ship. They had already thrown the Human bodies into a large pile that a Grunt was attempting to light on fire.

"Huh looks like we have something in common. They're taking their dead at least they're not completely heartless." James muttered noticing their pained looks.

"According to EDI's scans they have two hearts," Ashley said motioning towards the Elites

They turned and watched as two circular platforms were raised up on some sort of anti-gravity lift. After they were raised a Jackal stepped onto the platform on the ground and floated up a beam in the center. They came to a rest on top of the platform and began using their perch to scan the area. The smaller, aliens which had been coined with the term Grunts, carried small turrets of some kind to where ever the leading Elite told them to. Meanwhile a few Jackals walked into the base carrying splicing equipment.

"Alright, Ash try and take out as many back here. James lets go give them hell."

"About damn time we went on the offensive," James muttered sliding down the hill following Shepard. Ashley laid down getting into the prone position before she began aiming for the two Jackals in their nests. As soon as her finger hit the trigger killing the first Jackal all hell broke loose. The second Jackal jumped behind cover in his nest before she could get a shot on him. The grunts began to panic and a few broke rank and began to run. They were immediately stopped by the lead Elite Ultra who threatened to kill them with their own skulls should they ever run in fear. The Ultra immediately barked orders telling his remaining sniper to find the enemy sniper and his Kig-Yar infantry to move forward. Their shields would protect them should the sniper fire again and allow for their location to be known. The rest all jumped into cover behind containers and rocks with only the Sangheili standing their ground.

This would prove fatal as Shepard jumped out of cover behind a rock and fired on the closest Elite; James leaned past a rock opposite Shepard and fired on the same Elite. With the combined fire from their assault rifles and Ashley's sniper fire they were able to drop the alien's shields quickly. It jumped back though out of their line of fire, the Sangheili believed himself to be safe. His shields would recharge and then he would join his brethren and charge the Humans behind their cover. His shields never recharged though as he was blasted from cover by a concussion shot from Shepard's rifle.

The shot was able to take down the Elite, but Shepard had taken a close call to do it. His shields were down almost as soon as he leaned out of cover. 'Damn' he thought 'need to watch their fire'. Ashley continued to fire at any Grunt or Jackal that stuck its head out long enough for her to aim. The Jackal sniper was focusing more on Shepard and James, keeping them pinned, instead of on her. She wasn't able to get a shot off at it though until it finally tried to aim at her. The Jackal pulled out of cover and searched the hill through the scope of his Carbine looking for the Human sniper. No sooner had he spotted the Human than a bullet shot through his rifle and straight down his throat severing his spine and spewing purple blood over the nest.

Shepard and James continued to stick their heads out of cover and fire at the aliens, they were never able to get more than a few shots off at a time but they prevented any of them from advancing. Ash had managed to take out the Jackals with the hand shields, her advantage being the height of the hill allowing her to shoot them over their shields. She was now focusing on the Grunts with the plasma turrets, however due to their position behind containers she couldn't do anything but try and shoot at their feet scaring them more than anything. However it was enough for Shepard and James to gain a clear shot at them without return fire.

"Ever get tired of this?" James said pulling back into cover for his shields to recharge and to slap another clip into his rifle. "Cause I sure as hell don't!" He leaned out and fired again, an Elite had jumped out of cover and was attempting to rush them. James fired a carnage shot which cause the Elite to stagger long enough for James and Shepard to combine their fire. The shields went down even faster thanks to Shepard's disruptor ammo. With the shields down the Elite burst into flames due to Jame's incendiary ammo.

With most of his troops now dead the Ultra began to panic, they had been preparing for retaliation but none of them expected there to be anyone left alive on the planet aside from them. These Humans were clearly trickier than he anticipated. He looked to the only remaining Sangheili left under his command. It was the Sangheili way to die an honorable death in battle. But this was shameful; they had cowered behind crates leaning out to shoot only to duck back again. He had feared one of these humans would have been wielding that demonic blue power that could move and incapacitate large groups if soldiers. He had found only a few of their military units to posses this power; these humans had no such abilities. Growing confident that the two of them could easily charge the humans the Ultra ordered the Minor to charge first and take the darker skinned human on the right. He would take the one who wore black armor.

Jumping from their position both Elites ran towards Shepard and James. With the Minor leading they again focused their fire on him. The Elite tried to fire his plasma rifle back at them but found after a few shots it was dead. It mattered not, he would easily be able to kill one with his bare hands. He tossed the weapon aside and began to sprint at full speed. Shepard knew they would reach them long before the first one's shields were drained. He had faced many aliens but he didn't feel confident on taking them on hand to hand. He quickly pulled a grenade and chucked it at the duo. The Minor had instinctively grabbed the object before it hit him, he did not intend to grab it or hold onto it. It was a reflex; he realized his mistake and quickly tried to chuck it as soon as he had touched it. The frag grenade exploded before the Minor could let go causing the remainder of his shields to deplete and the shrapnel to lodge into his chest ensuring his death. The Ultra behind him was caught in the blast but only lost half of his shield.

The Ultra was in a rage now, he drew his energy sword and charged straight out of the smoke caused by the grenade to Commander Shepard. The Humans were surprised that he had survived the grenade thinking that such a close proximity would surely kill him. They didn't know his shields were stronger than the Minors. As the Ultra reached Shepard he thrust his sword straight at the his chest. He was stopped just inches by Shepard's quick thinking. He had brought his assault rifle up just in time to catch the Elite's sword. The weapon was cut clean through causing unrepairable damage but saving Shepard's life.

"Shepard!" Ash shouted over the radio not knowing exactly what was happening. Shepard jerked the rifle taking it and the sword and throwing them to the side. The Elite howled he activated his small wrist plasma knife and launched his fist towards the Human. Neither James, nor Ashley were able to get a shot on the alien without the possibility of hitting Shepard. Instinctively Shepard brought up his right arm to block the incoming attack. He activated his omni-tool blade and clashed arms with the Ultra.

As the Ultra forced his arm down on Shepard forcing him to his knees James quickly ran and jumped onto the alien's back. The Ultra stood up, he reached back with both his hands and threw James in the opposite direction nearly knocking him unconscious. Before he could turn again Shepard was already up and bringing his arm back for a powerful cut. Right as the Ultra turned around Shepard's blade cut through him spewing the purple blood over the Commander's armor. He twisted his arm to ensure the Elite's wound was as large as possible. He pulled his arm back and watched as the Elite simply fell to the ground lifeless.

James had gotten back up and bent over as he coughed up some blood. "Damn loco that was one hell of a move."

"You alright James?"

"Yeah just a flesh wound."

Shepard took his word for it and, without pause, began searching for a new weapon to replace his assault rifle. He looked over the battle field littered with bodies and alien weapons. 'Well at least there's plenty to choose from' he chuckled to himself. He grabbed a carbine out of the Covenant container, based off their earlier recon it was a good small to medium ranged weapon. EDI had been able to write program that would allow the entire squad to see the level of the power cells or ammo that was left in any of the weapons just like they would with their own.

"Ash watch our backs we're going in the base make sure no one follows." Shepard said into the radio waving to Ashley to assure her they were alright.

Shepard ordered James to check for survivors, all that remained were a few unfortunate Grunts who panicked and ran at the sight of their enemy. After ensuring the Phantom drop ship was devoid of any live aliens, the pair headed into the Alliance base. After killing the only remaining Grunt minor in the base they passed the first of only two rooms in the building. The majority of the facility was underground, topside there were only a few other buildings the mess hall and bunks. The main building contained only a security check point followed by another room with an elevator.

The Covenant were attempting to cut open the door but to no avail. Shepard activated his omni-tool and attempted to contact the squad left stranded in the ruins. "Church! We've been able to clear all hostiles we need you to unlock the door."

The door's holographic lock turned green as his radio flickered to life _"Commander is that you?... glad to hea..."_

"There's too much interference, Ash we may lose you while we're down there."

_"Just be careful, I don't want to have to save both your asses."_

"Why do you have to save my ass? I don't know if you saw but I saved Shepard pretty good back there," James said mockingly.

They stepped onto the elevator after it finally reached the surface. The ruins were several hundred klicks underground. Whatever it was, it was large and very old. For some reason the Alliance had sought the need to keep it completely hidden not only from the Council but also many of their own high ranking officers. This was the reason the Covenant had attacked Humanity, and Shepard sure as hell wasn't leaving without knowing what was so damn important.

After descending for nearly 10 minutes the elevator began to slow as it reached to base level. As the door slid open they were greeted by the end of a barrel. Pulling their weapons instinctively James and Shepard realized the weapons were wielded by Alliance Marines.

"It's the Commander lower your weapons," Church said pushing Manny's rifle down "Damn good to see you Commander, we couldn't tell if it was you or some alien trap." Church stepped forward and held his hand out for the Commanders.

Holstering his Carbine Shepard shook his hand and stepped out of the elevator. They were currently located in an underground cave with the only exit in the far back in complete darkness. There was no natural light, instead excavation lights were scattered about the site.

"Glad to see you were able to clear them out topside, we lost a lot of good people defending this place."

"Good to see your squad made it out alive," Shepard commented trying improve upon Church's morale.

"Some of us did anyway," Church began walking towards the back of the cave. "Ruins are this way the info you want will be in the lead research lab located near the top of the tower."

"Tower? Who the hell would build that underground?" James said as he and Shepard followed suit.

"Don't know doesn't look Prothean or any other known civilization. Probably why the Alliance kept hush hush about it." Erin said as she brought up the rear of the group leading into the cave.

"What we do know is it's old and still has some operational power," Samuel added

Once they passed through the darkness of the tunnel the cave immediately opened up revealing a vast open area with an impossibly massive structure to their right. The building covered the entire width of the cave, with a single tower several stories high. The walls were angular in shape with parts glowing bright with some sort of neon light at the crevices. It wasn't anything like the Covenant with their purple rounded ships, it looked almost Prothean with a simple design highlighted by the lights. Protheans however never made anything on this scale and their structures were simpler far simpler looking than this. No this structure was something all together something much more advanced than any known civilization; it showed no sign of age or tear. It looked as though it had been built yesterday.

"Don't worry the tower has a working elevator of sorts, shouldn't be too hard to reach the top," Manny said talking for the first time since Shepard had met him.

"Why didn't you already have the data if you know where it is?" James questioned Church

"We didn't have the access code for the Science geek's terminal," Church said looking to Shepard. "I'm assuming you have some sort of plan for that?"

"Our AI wrote a decryption software, should be able to get through any fire wall," Shepard said leading the group toward the structures only door. It slid open as they approached.

"Aren't AIs illegal?"

"Long story, short version Cerberus made her," James said ending the discussion.

As they walked down the hall towards the floating platform a mechanical drone greeted them. It was are grayish-white in color, and had two arm-like appendages with two grapple fixtures at the end of each arm, along with some sort of central head and a curved undercarriage containing a weapon.

"They won't bother you, we call 'em Sentinels. Harmless really but they have a nasty beam that'll burn you to a crisp should you tamper with anything they don't want you to." Church said pushing past the floating machine. "We didn't have much access down here but according to the science geeks at the mess hall they're supposedly friendly."

"What do you mean they don't want you to?" Shepard inquired still glancing back at the Sentinel which did its equivalent remaining in place.

"Docs used to say they would help with the studies. Even led them to some unknown areas of the facility," Manny answered. His tone changed mockingly as if he were saying a story around a campfire. "But one day some poor curious bastard decided to look around without the Sentinels, found a locked door. Surprising considering every other door and terminal activated with the simplest touch. So his curiosity peaked he decided to manually open the door, once he touched it though every Sentinel immediately glowed red and became hostile. Two quickly cornered the doc and left him a pile of ashes, then carried on as if nothing had occurred." He continued leaning in close to Erin attempting to gain a laugh

Erin slapped him out of her face, they both chuckled. This childish humor helped to distract them from the recent deaths plaguing all of their minds. "Orders after that were anyone coming down here didn't stray from the Sentinels path and leave that door alone. A couple of eggheads took some tools and tried to see what was on the other side without opening the door. All they could tell was a medical lab of some kind," Sam explained as he slapped Manny in the back of the head for acting like a child.

"Elevators just past this door sir," Church said stepping aside to let the Commander walk through.

Once they were all in the room and on the elevator it began to rise and quickly, it appeared to simply lift through thin air faster than any elevator Shepard had been on. And this one didn't even feel as though it was moving. If it wasn't for the passing walls there would be feeling of movement.

"Well that's a new one," James said leaning over the platform eyeing the ground cautiously. They reached the top in mere seconds, the top room of the tower looked as though it were a command and control center. There was a small platform in the center along with other consoles along the far wall; it reminded Shepard of the CIC on a ship. There were Alliance computers and lights scattered about showing clear signs of use. Shepard moved over to the computer attached through a wire to the consoles. After running the encryption he began downloading all the data he could onto his omni-tool.

"Ah damn this is so cool," James said bending over the alien console touching the holographic buttons.

"Don't touch..." Shepard stopped as the platform in the center showed a large hologram. It was a galaxy, obviously theirs as it showed the location of Harvest. Suddenly it zoomed into a cluster several hundred light years away from any known Relay. It zoomed in further revealing some sort of system before focusing solely on a large gas giant.

"It's a map?" Erin said questioningly.

"The question is what's at the X"

**AN: **Well this is by far the longest chapter yet, and I fell it is the best so far. Hopefully there is improvement in my writing, I'm making sure their actions are explained and how they're doing them. If you have any suggestions please let me know.

I'd recommend you going back to Ch 4 as I updated it after its publication with a quick AN. It's a sort of vote as to who you'd like as the romance for ol Shep in this story. Won't affect it much but can help with someone's personal taste or preference. More details can be found at the end of Ch 4

As always thanks for reading


	6. Chapter 6 Almost There

Ch 6

Almost There

Fleet of Particular Justice

9th age of Reclamation

Thel 'Vadamee paced the bridge of his flagship. His fleet had arrived in the system shortly after the Jiralhanae vessel discovered it. The newly appointed High Prophets had personally ordered the destruction of any Humans on the planet, and the location of any holy relics to be found and taken from the Human's grasp. Thel had been hand selected to lead this attack, he was monitored by a single Minor Prophet. Who continued to aggravate Thel by insisting the Fleet's main force remain back so to prevent any Holy relics from being destroyed. Instead the Prophet foolishly allowed Human vessels to escape the planet carrying survivors. Only limited glassing would occur on the Human cities allowing for more to escape and live.

"You are wasting my time Prophet. If you do not allow me to deploy more forces the Humans," Thel Vadamee spit the word out in disgust. "Will seize the archives and destroy them."

There on the central platform of the Assault Carrier's bridge sat the hologram of the Prophet. He was on another carrier ensuring his orders were followed. Thel 'Vadamee had contacted him again to argue against his plan and orders.

"You may send more ground forces but there shall be no more destruction of the planet until we uncover the nature of the Holy ruins." The Prophet look cross towards the Sangheili.

"Of course, by your command Holy One," Thel said with an air of hatred in his voice. He cut the transmission replacing the Prophet's hologram with that of the fleet's current position and the planet's location.

"How many Scarabs are still in the ship's hanger?" Thel said towards the ships computer intelligence, the simple minded AI that ensured the less vital systems were operating properly.

"Three" it responded coldly.

"Excellent." He ordered for the hanger to be hailed. "Send a Scarab to the ruins, along with ground support to access the archives underground."

'That fool of a Prophet will not prevent the success of this fleet.' Thel thought to himself as he sat in the bridge's command chair. The monitors showed the scarab being launched towards the planet along with drop ships following behind. 'We will take control of the archives and then focus on burning the filth off this planet'

Harvest: 4 Months till Reaper invasion

The entire cave system shook, shaking the structure and everyone inside. Everyone grabbed a wall to steady themselves until the quake subsided. Shepard checked back to his omni-tool ensuring the download was complete and they had the data needed. He grabbed his rifle and quickly motioned for the door. The entire group moved quickly with a purpose running towards the elevator.

As it began to descend the cave shook, the group braced themselves with everyone crouching to avoid falling. The platform finally reached the bottom with several more shakes along the way. After exiting the structure the group dashed straight to the elevator back to the surface. All the while the shakes grew stronger causing dust and debris to fall from the cave's ceiling.

After reaching the surface the group drew their weapons when the door slid open. Ensuring the room was clear they all sprinted outside, all the while the ground continued to shake.

_"Shepard!" _Ashley shouted over the radio. She could see them exiting the base from her position on the hill overlooking it.

"I see you, tell Cortez he'd better have the shuttle ready!"

_"We've got bigger problems," _Ashley said as she stood up from her prone position and began jogging towards the group. The rest of them all turned their heads to see the problem. They found the cause of the shaking, a massive four legged walking tank. It was moving slow each of its steps causing the ground to thud and shake. It looked like a bug of sorts, its rear possessed a massive cannon that sat on top of a platform. The entire vehicle looked like some sort of beetle.

"We got reports about those things, very tough and very mean. We called them Scarabs," Church said as he pulled out his helmet placing it back on his head. "Large AA gun in the back, the head has some sort of beam weapon."

"What are your orders sir?" Sam asked hoping Shepard would have some sort of plan.

"We won't be able to call for evac, too risky..." Shepard panicked they only had small arms, nothing large enough to take out something that heavily armoured. They could either fight the best they could or run underground and hold out only a bit longer. "We may have to make a run for it unless..."

Shepard formulated a plan, the Scarab was slow and hadn't noticed them yet. It would be another ten minutes before it would be able to see clearly what happened at the base. The Phantom drop ship was still on the ground, they would never be able to run in it as the Scarab would most likely shoot them down without hesitation.

"No the only way we're getting out alive is if we take that thing out."

"What! You can't be serious," James stuttered "Look at the size of that thing!"

Manny spoke up "He's right the only hope we have is to run like hell."

"Won't make it that thing will catch up soon enough," Erin said beginning to sound panicked

"We take that shuttle, get in close and take that thing down from the inside," Shepard said heading towards the shuttle.

"Do you know how to fly this thing?" Church said motioning for his squad to jump in. After pushing out the small pile of carcasses the entire group boarded the shuttle and began to strap in. Shepard walked to the cockpit followed by Ash, meanwhile Church ordered Manny and Samuel on the door guns on the right. After settling to the large seat Shepard activated the shuttle.

"You never did answer him," Ashley muttered taking the seat next to him.

"No need to have him worry, EDI mind telling me how to fly this thing."

_"One moment Shepard," _EDI said as she began to scan the shuttle's controls using Shepard's and Ashley's head cams. _"I'd recommend pressing that button."_

Shepard's helmet display highlighted the button and after pressing it the ship immediately shot up. EDI continued to give Shepard instructions on the controls. After a moment he was able to get the hang of it. He closed the sides of the shuttle and began to steady out.

_"The Scarab is attempting to hail you,"_ EDI informed him as Shepard turned the ship around to face the machine.

"Try and assure them we're friendly."

_"They're allowing you to pass, however once you leave the plotted course they will know."_

"I hope your plan works here Skipper," Ashley said pushing against the wall to brace herself in the chair.

As Shepard approached the Scarab he slowed the ship down. After pausing for a moment he dropped the side hatch allowing for the entire squad to open fire on the few unfortunate Elites standing on the top and centre level. After their ambush succeeds everyone jumped onto the still moving Scarab as Shepard attempted to level and keep it in line with the Scarab.

Their luck soon ran out as the Scarab stopped moving and instead aimed its AA gun directly at the Phantom. Shepard had no manoeuvring room, the plasma hit the ship nearly dead on and caused it to spin out of control. Quickly running to the exit Shepard braced himself as the Phantom swayed back towards the Scarab. He jumped right before the drop ship sank to the ground barely managing to land on the upper platform.

The rest of his group were on the platform below, Sam had detached a plasma turret from the side of the Scarab and was surprisingly able to carry it with little difficulty. They still had movement on their trackers, most likely the pilot and crew remained on the lower deck. After sliding down onto the left side of the ramp that proceeded to the lower deck, Shepard motioned for Sam to go first and begin suppressing fire.

After killing only a single Grunt, Sam began walking firing the turret to keep anything else pinned. Shepard was a step behind him, and once they reached the bottom pointed for him to turn left while he tuned right. There only remained a single Elite and Grunt left, they had their backs against a glowing wall and fired once they saw their enemy. Shepard silenced the Grunt with two shots from his Carbine to the Grunt's chest and a finale one to his head. Sam focused his fire on the Elite, whose shields quickly dropped causing the alien to flinch and finally die from the sustained fire.

With every remaining alien on the Scarab dead Shepard assumed it would be out of commission. There were no cockpits or hatches, and yet the Scarab began to move again. The sudden shake caused Shepard to lose his balance and fall. After picking himself back up he ordered everyone to search for survivors. Erin nearly fell off as she walked along the side towards the back, but after a second everyone reported the same thing all clear. The Scarab seemed agitated now. It was beginning to shake violently as if it were attempting to shake off Shepard and his squad.

"EDI how the hell do we take this thing out!"

_"There is some shielding near the rear, it must be protecting some sort of power supply."_

Shepard rushed back and found Erin leaning against the wall near an odd circular force field. After the two of them combined their fire the shield quickly fell. However the Scarab continued to shake, the entire group were bracing against walls or the floor holding on for dear life. Shepard and Erin again fired at the odd power supply that was behind the shield.

After a short moment of firing Shepard noticed that the power supply was bleeding. Orange worms were begging to fall as the object exploded causing the Scarab to stop and buckle to the ground.

"Move now!" Shepard ordered as an alarm blared and lights flashed red. Everyone jumped off the Scarab and ran in opposite directions. Not a single one dared to look behind as the intense heat from the explosion blasted them all off their feet. All of them luckily survived with nothing more than a few scratches. The wrecking hull of the Scarab now sat with blue flames rising from it and a few pieces of metal fell from the sky.

"Cortez..." Shepard grunted as he sat down on a small rock while the rest of his squad began to pick themselves up. "Come pick us up."

Shepard removed his helmet running his hand over his head and face. Sweat dripped onto the dirt as the heat from the fire grew slightly brighter. He had survived and completed the mission, and even more miraculously been able to do it without any losses. But every muscle and bone ached, never had he been forced to fight this hard. Not even the Collectors took this much to take down.

Cortez's Kodiak began to appear still fresh with damage. It landed not twenty feet from where the Commander sat. The door opened and Cortez stepped out, he helped everyone else onto the shuttle all of which were as tired as Shepard. Finally Shepard stood up and began to limp to the shuttle.

"Commander, you had us all a bit worried there for a second," Cortez joked as he assisted Shepard into a seat.

He grunted in response. Cortez returned to the cockpit and began flying the Kodiak back to the awaiting Normandy still hiding in orbit. James had fallen asleep on Ashley's shoulder who had leaned against the door completely passed out. Manny took up two seats across from Shepard, he was curled up into a ball grunting, he had taken some shrapnel in his stomach that left nothing more than a bruise. Sam sat across from Shepard with Erin asleep in his lap. He was one of the few awake and conscience. Church sat in the seat next to Shepard, he was already working on his omni-tool listing the dead and missing.

"I never did have the chance to thank you sir," Church said lowering his arm. "Without you we may have ended up dead."

"How many men did you lose?" Shepard asked.

"Three in my squad, they were good people. We were a family, only the best got in this squad. All N7s all willing to go above and beyond. Last time we lost anyone was over a year ago fighting some slavers. Erin was his replacement, she's still the greenest of us here."

"You lose people, it's one of the hardships of command. I had to leave a good friend behind, I piratically ordered him to his death. It's a pain I wouldn't wish on anyone, but still one that needs to be done."

"We just never got this badly slaughtered."

"Approaching the Normandy Commander," Cortez informed Shepard. After standing up he griped the railing, the Kodiak floated in and after the shuttle bay was sealed and re pressurized the shuttle's door opened. Shepard shook his squad awake, they would all most likely shower then immediately hit the bunks. Even Church looked like he could pass out at any minute. They all dragged themselves to the elevator with Cortez having to help James back to his feet when he tripped over the work station.

Shepard still had work to do and while the squad dragged themselves off the elevator at the crew deck, he continued up and went to the communications room. Admiral Anderson's and Admiral Hackett's hologram were already present. Anderson had left Udina in charge of negotiating with the Council and the full extent of their support. Meanwhile he would prepare Earth while Hackett mobilized the Fleets and returned them all from previous engagements.

"Shepard, it's good to see you in one piece," Anderson said surprised never having seen the Commander in such an exhausted state.

"Good to see you too Anderson."

"Sorry didn't expect you to look so beaten."

"Commander I heard you were able to get the Intel," Hackett said ending any pleasantries.

"I did."

"And what exactly was worth all this trouble?" Hackett asked. He was one of the few who knew about the facility but never learned more than its location.

"A map."

AN: Well hot damn this is going well. I again hope that there is improvement in the writing, I'm focusing really hard on describing the details as much as possible but I did encounter some trouble with the Scarab scene. If you've played Halo you know how confusing it can get while on one of those things making it difficult to describe.

Now on to other topics, I've noticed in my review that I either get "Oh this is good", some sort of random fact from a wiki, and not much else. I've yet to see anyone completely say this story is terrible. And when I first started writing it I got several tips on how to improve, but now nothing. And yet I've gotten very little reviews and follows compared to many other stories. Now I know this is my first time writing an actual story but I feel that this isn't nearly as bad as some of the other stories out there. And I've yet to write something that was so unbelievably outside the lore that it's impossible. So far everything I've written has come from extensive research into both sides as to how the physics would work. (Once I get to Halo 2 stuff it may get a little farfetched). So please if you are reading this follow, review and tell me what you want or think needs done. I've yet to receive any votes as to a love interest.

One last thing before I sign off, I need MASSIVE help. I've got the timelines of both trilogies worked out and how they will go together. But I need help on the ending. We all know that ME ending could use some work, however including halo may be able to fix that. So tell me how you think this will end and the next chapter will have another vote thing to help allow me to find out where exactly I want to take this. I have planned this thing through and every plausible ending I've gotten a pretty good idea for but I'm not 100% solid on it.

As always thank you for reading.


	7. Chapter 7 Halo

Ch 7

Halo

In orbit above Harvest

4 Months till Reaper invasion

"That's all there was?" Hackett questioned with a tone of anger.

"All that was worth knowing," Shepard said leaning over the rail in front of Hackett's hologram.

"What do you think our next move should be, Shepard?" Anderson said while checking the intel info after EDI had sent it. "This system is far from any Relay it would be months before a ship could reach it then return."

"Which is why the Normandy should be the one to do it," Hackett answered him. "One of the fastest ships we have and one of the few we can spare."

"You can't expect the entire crew to just sit in FTL and chase down what could be nothing," Anderson said flustered.

"That nothing started a war, they sent nearly 700 soldiers to the base before it fell. They wanted that map, and whatever is there we need to find first," Hacket said defending himself.

Shepard interjected his opinion, "We'll find it, whatever's there is completely alien to us. It could be the alien race that built the ruins, they could help us fight the Covenant."

"But why the Normandy? Something like this there should be scientist, diplomats, researchers! Not soldiers who will be needed fighting a war," Anderson pleaded throwing his arms to his sides in defeat.

"They'll figure out where this system is, and the'll attack anyone there with extreme prejudice. We need every available ship to begin preparing for defense. The Normandy is a scouting ship one that will be able to keep hidden," Hackett said ending the debate.

"Then good luck to you Shepard, and Godspeed," Anderson saluted as his hologram vanished.

"Shepard, head to Elysium and get resupplied. Then find out what the hell the Covenant are after. Hackett out."

Shepard leaned off the rail and began walking back towards the cockpit, still exhausted from the last mission he moved rather slow. He passed through the war room which was in a flurry as the Normandy tracked multiple Alliance war assets. There were reports of an unknown ship entering orbit around another colony that had multiple people running as they transferred the data to the rest of Alliance personal.

After passing through the security check point, Shepard walked through the CIC straight to Joker in the cockpit. He allowed himself to smile, Joker had been there with him through thick and thin. He was the last person Shepard saw before the Normandy was destroyed and he was killed. And Joker was one of the first to volunteer to help against the Collectors. Now there was no one else Shepard would rather have by his side.

"So just like old times huh?" Joker said as he piloted the Normandy to the Mass Relay and away from Harvest.

"Yeah, like old times," Shepard said with an air of pain in his voice.

"Hey are you alright Commander? You look exhausted," Joker turned his chair around to face Shepard. He never stood up if he could help it, the frailty of his bones caused by Vrolik Syndrome forced him rarely leave the cockpit.

"You know where to go Joker, I'm gonna go get some rest."

"You'll have plenty of time to do that, EDI said it'll take us a month and a half to get to... what's out there anyway?"

"That's what we're going to find out."

SR2- Normandy en route to unknown location

3 Months till Reaper invasion

Shepard stood up from his couch and stretched his arms and legs. Nearly a month they had been on the ship, only exiting FTL for discharges. So far the crew was barely coping. Nearly a month on a small ship in space can test even the toughest crew. Luckily they had plenty of food and water, and all systems were operating normally. EDI insisted on hourly checks to ensure that the Normandy wasn't being too stressed or strained.

Luckily everyone was adjusting fairly well, Church's squad had adjusted and been assigned as a cleaning crew. More of as a necessity, and they were the only ones without any assigned duties. Shepard had mainly been focusing on the War, everything had happened quickly he barely had time to stop and think. There was little else to do now. Shepard walked through his room and to the elevator. He would do his normal rounds and grab dinner before returning back to his quarters. '

'Terrible excuse for a meal really' He thought to himself as he hit the holographic that brought him to deck three. 'Raw space-cow has to taste better than the slop they have.'

The doors opened revealing the kitchen. Most of the crew grew stiff as one shouted "Officer on deck," and then all saluted. Shepard put them at ease before turning to the left towards the port observation deck. Going to the back room he found James, Samuel, Manny, and Erin along with a few other crew members all playing a round of cards.

"Couldn't find anything better to do James?" Shepard said coming up behind him and crossing his arms.

"Just having a friendly game Commander, no need to worry," James said as he placed his cards down. He'd lost the round and watched mournfully as the pot was claimed by Erin.

"Yeah nothing like a friendly little ass whooping," Erin said mockingly towards James.

"Just make sure I don't hear about anything tomorrow," Shepard left them to their game, smiling as he searched for the rest of his crew. It felt odd to him, ever since he first took control of the Normandy there had always been some alien or another running around. Whether it was Liara, Thane, or Garrus with his calibrations, there was never an all Human crew. He missed his old team mates, now more than ever.

He entered the sleeping quarters, there he found Ashley and Church sitting in chairs along the back wall against the window showing the FTL drive.

"Everything alright with you two?" He asked taking a third seat in between the pair.

"Fine actually, Ashley here was just telling me the most fascinating story about you."

"Oh really," Shepard asked leaning back with his arms cross looking at Ashley.

"Don't get so riled up Shepard, nothing bad," Ashley said glancing slyly towards Church who smiled and quickly broke eye contact

"Was it the time I saved your ass on Virmire, or when we rescued you from Eden Prime?"

"No I believe it had something to do about you trying to seduce some Asari serial killer," Church said laughing under his breath.

"You knew about that! And it wasn't a serial killer it was an Ardat-Yakshi, much worse,"

"Of course I knew about it, do you really think Joker wouldn't tell us about you trying to dance in a night club?" Ashley said rolling her head in laughter.

Shepard shook his head smiling. He stood up from the chair and left the quarters after warning Ashley that he also had dirt on her. He grabbed the slop of a dinner and returned to the CIC to see if Traynor had any new information.

"Actually Commander, I was hoping to get your opinion on something," Traynor said turning away from her terminal. Shepard placed his food on the railing before saying "Shoot."

"I've been looking over the data our scientist gathered from the alien ruins. The scientist seemed to think that it was some kind of research lab or data storage area. The thing is the only research that could of been occurring would have to be conducted in a lab, that's true with any civilization. There was only ever one lab found in the ruins, it was some sort of medical lab."

"What's the question,"

"Sorry not really a question, just an interesting observation. It occurred to me that they would most likely be studying some other alien species. Harvest obviously wasn't their home world and they were most likely a far reaching galactic government. But there are absolutely no traces of anything worth studying any where near that planet. It's far away from anything of value, it's almost as if they wanted to study something and took every precaution so if it were to escape it would cause very little damage."

"Do you have any hard evidence?" Shepard said his curiosity peaked.

"No most of it is just a theory, but EDI seems to agree."

"That would explain why a scientist was attacked trying to open the lab."

"Anyway nothing new to report sir. I'll just go back to my post," Traynor said as she turned around back to her terminal.

Shepard grabbed his food and went back to the elevator and returning to his cabin. He sat down at his desk and after finishing his meal loaded up an old 20 century computer program on his terminal. It was a sci-fi game in which a space ship moved along the bottom of the screen while alien insect shaped ships would swarm and attack. After finishing the 5th level, Shepard paused the program. He sat back and looked at the screen, his current situation seemed so similar to that of the space ship. Forced to fight an unwavering enemy, and once they were defeated another more dangerous enemy took their place. The question he asked himself was when do the enemies stop.

SR-2 Normandy unknown system

2 months till Reaper invasion

Shepard watched in the cockpit as the Normandy exited FTL. The entire crew had endured a difficult journey, and now all of them sat waiting to see what had caused such a long trip. As Joker slowed the Normandy down to sub-light speeds the ship shook and shuddered. It was small but still unnerving since the ship had never taken such a long journey without stop.

Immediately a gas giant appeared, it was the planet shown in the map. Only a single moon was visible from their side of the planet, along with something else. A single glimmer shined off the Sun's light, it was barely visible to the Human eye. EDI's sensors were able to detect it long before anyone actually saw it. Shepard turned around to the CIC and watched as the hologram depicting the Normandy was replaced with that of the Planet.

The hologram zoomed in, magnifying the sliver. What was shown astounded every crew member. In between the orbit of the planet and it's moon was a ring. A massive ring approximately 10,000 kilometers in diameter. The outside of the ring was metallic, with massive lights and machines running across it. On the inside it looked like a world, there were landmasses and oceans, covered in cloud cover.

The ring was a Halo

"Shepard we've got contacts, the Covenant beat us here," Joker said immediately springing the ship into action.

"Activate the Heat Sinks, maybe they haven't found us."

"They're ships are headed right for us. We need to take action," EDI's voice sounded worried and frantic, odd especially for an AI that had been to the center of the galaxy and back.

There were small Covenant docking ships, Phantoms equipped with docking tubes, were heading straight for the Normandy. "They're sending a boarding party? Why the hell don't they blow us out of the sky?" Shepard asked while thankful the Covenant had again underestimated them.

"Joker shoot them out of the water and get us on that..." Shepard was interrupted as the ship's communication systems began to blare. After a moment of static a transmission came through. In perfect English a computer generated voice said "We are the Covenant, you have defied the sanctity of the Holy Rings with your filth. Prepare to die in our cleansing fire!"

**AN: **AND BAM finally got that done, I wanted this to be part of Chapter 6 but I felt it would have been far too long then. So I decided to make an entire new chapter. The ending of this one kills me though, I couldn't figure out how to end it after I described Halo. I didn't want someone to say "Oh hey it looks like a Halo" because I've ended nearly every chapter with dialogue and I'd like to break that pattern.

So onto the rest of the story then, I've yet to receive any votes for a love interest. I know I only posted chapter 4 about a month ago but I know people are reading this story. I've seen the views go up every time I post a chapter and people read it all the way through, so either they hate the story or they choose not to post a review. I NEED reviews, the reviews I got in chapter 1 helped me to write better. The complaints I got when I first started this story a year ago pushed me to rewrite it. So reviews do help but please post them! I've seen stories in the same category that are just terrible, poorly written and cliched all to hell. And yet they get 5 or ten reviews saying "Oh great story" and then 15 more reviews on how to make it better AFTER ONLY POSTING 1 CHAPTER! And I've had several chapters with not a single review for or anything! So please help me out I've tried to entice reviewers with the contest and now I'm going to entice more...

If you can guess what game Shepard was playing then you will get a HUGE CASH PRIZE! (not really) Otherwise please tell me how you'd like me to fix ME3's ending and what love interest you want. More info on the love interests can be found in Ch 4.

As always thanks for reading

**EDIT: **Thank you to the guy who actually reviewed this story, thanks to your review I've gone back and fixed the ending. I knew it wasn't that good but I though I'd wait to see if anyone would actually complain about it. And that is why people should review so I can go back and fix parts of the story that need it or need editing.


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